Influenza Bern

Methoods

Incidence and Reproduction number ( R effective)

  • Incidence per 1’000 inhabitants
  • Rolling average over 3 weeks
  • Calculation of effective reproduction number (R effective) using rolling average
  • Only include cases > 5 (otherwise huge R)
  • R package: EpiEstim
  • Weekly data, not daily
  • serial interval—the time from illness onset in a primary case (infector) to illness onset in a secondary case (infectee)
  • Mean and standard deviation of the serial interval = 1 week, but maybe = 3 days, sd= 1 days would be better
  • But I cannot define values < 1, e.g 3/7
  • However, 1 week is not that bad as assumption for “mean serial interval” (e.g. SARS 8.4 days, first SARS-COV-2 estimations 7.8 days, later studies 4 days)
  • R effective estimated with 3 weeks -> R effect with weekly data? Possible? Not too much noise?

Maps - Municipalities

  • calculated only for pandemic times:
    • 28.06.1918 - 20.06.1919
    • 09.01.1920 - 18.06.1920
    • 06.01.1922 - 21.04.1922
    • 04.01.1924 - 06.06.1924
    • b1.11.1924 - 08.05.1925
  • Incidence:
    • breaks: Jenks Natural Breaks - finds the “best” way to split up the ranges.
    • natural breaks minimizes the variation within each color, so the areas within each color are as close as possible in value to each other
    • quantile breaks do not work, because there are many zeros in the municipalities from 1920 onwards
  • Hotspots:
    • local spatial statistic G
    • R package: spdep
    • returned is a Z-value
    • high positive values indicate the posibility of a local cluster of high values
    • low relative values a similar cluster of low values

Canton Bern

Regions of Bern

Incidence

Reproductive Number

Municipality

1918 First wave

1918-1919 second wave

1920

1922

1924

End 1924 -1925

Gif